Here are a couple of real errors that FlightCrew missed 100%. Said NO ERRORS FOUND. But, epubcheck 3.0 found them both.

Code:

Validating against EPUB version 2.0
ERROR: The Curse of the Mistwraith.epub/OEBPS/content.opf(86,103): filepos1731098': fragment identifier is not defined in 'OEBPS/Text/copyright.html'
ERROR: The Curse of the Mistwraith.epub/OEBPS/content.opf(87,92): 'filepos250': fragment identifier is not defined in 'OEBPS/Text/title.html'
Check finished with warnings or errors

Here is the OPF with the errors. The two errors are in the guide section.

Spoiler:

<?xml version="1.0" encoding="UTF-8" standalone="yes" ?>
<package xmlns="http://www.idpf.org/2007/opf" unique-identifier="uuid_id" version="2.0">
<metadata xmlns:dc="http://purl.org/dc/elements/1.1/" xmlnspf="http://www.idpf.org/2007/opf">
<dcublisher>Voyager</dcublisher>
<dc:description>&lt;div&gt;&lt;p&gt;The stunning first volume in Janny Wurts’s epic tale of two half-brothers cursed to life-long enmity, now re-released with a striking new cover.&lt;/p&gt;&lt;p&gt;The world of Athera lives in eternal fog, its skies obscured by the malevolent Mistwraith. Only the combined powers of two half-brothers can challenge the Mistwraith’s stranglehold: Arithon, Master of Shadow and Lysaer, Lord of Light.&lt;/p&gt;&lt;p&gt;Arithon and Lysaer will find that they are inescapably bound inside a pattern of events dictated by their own deepest convictions. Yet there is more at stake than one battle with the Mistwraith – as the sorcerers of the Fellowship of Seven know well. For between them the half-brothers hold the balance of the world, its harmony and its future, in their hands.&lt;/p&gt;&lt;h3&gt;From Publishers Weekly&lt;/h3&gt;&lt;p&gt;What promises to be a rather standard epic fantasy commences with this book, volume one in a series called The Wars of Light and Shadow. In this installment, two magic-wielding half brothers are forced by an evil geas (a delayed compulsion spell cast by the incorporeal but sorcerously potent Mistwraiths) to battle each other, nearly ripping their kingdoms asunder in the bloody fray. Arithon, Master Mage and keeper of the shadow-half of the royal magic, is a compassionate man who is constantly battling his sensitive musical nature as he struggles to come to terms with the job of ruler, which he does not want. His brother Lysaer has the power to focus light; a charming man and born ruler, he becomes cunning and devious after the Mistwraith's spell is activated. Events in the heavily foreshadowed plot conspire against the royal duo, until they are forced to pit jaded townsmen against noble barbarians in a punishing and debilitating war. They are aided in their travails by a young enchantress, Elaira, a spunky role model sure to become beloved as the series progresses, and by many wise and quirky sorcerers. Forced to do duty as a harbinger of many volumes, this tale is plot-heavy, but there are hints of the appearance of unicorns and other mythical, crowd-pleasing wonders in later installments. Veteran epic-writer Wurts ( Mistress of Empire ) brings the breadth of her experience to bear in an entertaining and readable--though not outstanding--story. &lt;br&gt;Copyright 1993 Reed Business Information, Inc. &lt;/p&gt;&lt;h3&gt;From Library Journal&lt;/h3&gt;&lt;p&gt;Two brothers, heirs to lands and locked in a blood feud, are drawn across a dimensional portal into a world where they are hailed as the promised saviors. As Arithon, the Master of Shadows, and his half-brother Lysaer, the Lord of Light, prepare to do battle against the Mistwraith, who has for centuries cloaked the world of Athera in darkness, they face an additional battle born of their mutual distrust of each other. Although fantasy author Wurts breaks no new ground in this series opener, her elaborate and vivid world-building and complex protagonists recommend this title to fans of epic fantasy.&lt;br&gt;Copyright 1994 Reed Business Information, Inc. &lt;/p&gt;&lt;/div&gt;</dc:description>
<dc:language>en</dc:language>
<dc:creator opf:file-as="Wurts, Janny" opf:role="aut">Janny Wurts</dc:creator>
<dc:title>Wars of Light and Shadow 01 - The Curse of the Mistwraith</dc:title>
<meta name="cover" content="cover"/>
<dc:date>1993-01-01T00:00:00+00:00</dc:date>
<dc:identifier opf:scheme="ISBN">9780586210697</dc:identifier>
<dc:identifier id="uuid_id" opf:scheme="uuid">c8b3791c-f21f-418e-a44c-ca259eaca0bf</dc:identifier>
<meta name="version" content="5.1"/>
<meta content="0.6.2" name="Sigil version"/>
</metadata>
<manifest>
<item href="Images/cover.jpeg" id="cover" media-type="image/jpeg"/>
<item href="Images/00003.jpeg" id="id3" media-type="image/jpeg"/>
<item href="Styles/stylesheet.css" id="css" media-type="text/css"/>
<item href="Text/title.html" id="title.html" media-type="application/xhtml+xml"/>
<item href="Text/title2.html" id="title2.html" media-type="application/xhtml+xml"/>
<item href="Text/prologue.html" id="prologue.html" media-type="application/xhtml+xml"/>
<item href="Text/ch01.html" id="ch01.html" media-type="application/xhtml+xml"/>
<item href="Text/ch02.html" id="ch02.html" media-type="application/xhtml+xml"/>
<item href="Text/ch03.html" id="ch03.html" media-type="application/xhtml+xml"/>
<item href="Text/ch04.html" id="ch04.html" media-type="application/xhtml+xml"/>
<item href="Text/ch05.html" id="ch05.html" media-type="application/xhtml+xml"/>
<item href="Text/ch06.html" id="ch06.html" media-type="application/xhtml+xml"/>
<item href="Text/ch07.html" id="ch07.html" media-type="application/xhtml+xml"/>
<item href="Text/ch08.html" id="ch08.html" media-type="application/xhtml+xml"/>
<item href="Text/ch09.html" id="ch09.html" media-type="application/xhtml+xml"/>
<item href="Text/ch10.html" id="ch10.html" media-type="application/xhtml+xml"/>
<item href="Text/ch11.html" id="ch11.html" media-type="application/xhtml+xml"/>
<item href="Text/ch12.html" id="ch12.html" media-type="application/xhtml+xml"/>
<item href="Text/ch13.html" id="ch13.html" media-type="application/xhtml+xml"/>
<item href="Text/ch14.html" id="ch14.html" media-type="application/xhtml+xml"/>
<item href="Text/ch15.html" id="ch15.html" media-type="application/xhtml+xml"/>
<item href="Text/ch16.html" id="ch16.html" media-type="application/xhtml+xml"/>
<item href="Text/ch17.html" id="ch17.html" media-type="application/xhtml+xml"/>
<item href="Text/ch18.html" id="ch18.html" media-type="application/xhtml+xml"/>
<item href="Text/glossary.html" id="glossary.html" media-type="application/xhtml+xml"/>
<item href="Text/ack.html" id="ack.html" media-type="application/xhtml+xml"/>
<item href="Text/about.html" id="about.html" media-type="application/xhtml+xml"/>
<item href="Text/byjannywurts.html" id="byjannywurts.html" media-type="application/xhtml+xml"/>
<item href="Text/copyright.html" id="copyright.html" media-type="application/xhtml+xml"/>
<item href="Text/aboutpublisher.html" id="aboutpublisher.html" media-type="application/xhtml+xml"/>
<item href="Text/titlepage.xhtml" id="titlepage" media-type="application/xhtml+xml"/>
<item href="toc.ncx" id="ncx" media-type="application/x-dtbncx+xml"/>
<item href="Fonts/CharisSILB.ttf" id="font1" media-type="application/x-font-ttf"/>
<item href="Fonts/CharisSILBI.ttf" id="font2" media-type="application/x-font-ttf"/>
<item href="Fonts/CharisSILI.ttf" id="font3" media-type="application/x-font-ttf"/>
<item href="Fonts/CharisSILR.ttf" id="font4" media-type="application/x-font-ttf"/>
</manifest>
<spine toc="ncx">
<itemref idref="titlepage"/>
<itemref idref="title.html"/>
<itemref idref="title2.html"/>
<itemref idref="prologue.html"/>
<itemref idref="ch01.html"/>
<itemref idref="ch02.html"/>
<itemref idref="ch03.html"/>
<itemref idref="ch04.html"/>
<itemref idref="ch05.html"/>
<itemref idref="ch06.html"/>
<itemref idref="ch07.html"/>
<itemref idref="ch08.html"/>
<itemref idref="ch09.html"/>
<itemref idref="ch10.html"/>
<itemref idref="ch11.html"/>
<itemref idref="ch12.html"/>
<itemref idref="ch13.html"/>
<itemref idref="ch14.html"/>
<itemref idref="ch15.html"/>
<itemref idref="ch16.html"/>
<itemref idref="ch17.html"/>
<itemref idref="ch18.html"/>
<itemref idref="glossary.html"/>
<itemref idref="ack.html"/>
<itemref idref="about.html"/>
<itemref idref="byjannywurts.html"/>
<itemref idref="copyright.html"/>
<itemref idref="aboutpublisher.html"/>
</spine>
<guide>
<reference href="Text/titlepage.xhtml" title="Cover" type="cover"/>
<reference href="Text/copyright.html#filepos1731098" title="Copyright" type="copyright-page"/>
<reference href="Text/title.html#filepos250" title="Title Page" type="title-page"/>
</guide>
</package>

I have found that using word2cleanhtml.com I often get an errant a href=(whatever), which is then closed out without any content. Flight Crew accepts that, but epubcheck will not. So I too have learned that while Flight Crew is faster, it is also necessary to go the extra step and run the finished booked through epubcheck.